ltnme: Gibbs sampler for LTN-based mixed-effects model

Description Usage Arguments

View source: R/ltnme.R

Description

a wrapper for gibbs_crossgroup

Usage

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ltnme(
  formula,
  data,
  test_baseline,
  niter,
  reffcov = 2,
  SEED = 1,
  save_alpha_only = F,
  gprior_m = 100,
  pnull = 0.5,
  lambda = 10
)

Arguments

formula

a lme4 type formula where the first fixed effect is the group indicator

data

a phyloseq object

test_baseline

the group to be used as baseline in the linear model

niter

number of Gibbs iterations

reffcov

specification of the precision matrix of random effects. 1: diagonal, 2: sparse with graphical lasso prior

SEED

random seed for initializing the parameters

save_alpha_only

whether to only return posterior samples of alpha(A)

gprior_m

hyperparameter in prior of beta with default value 100

pnull

prior probability of the joint null hypothesis with default value 0.5

lambda

shrinkage parameter in the graphical lasso prior with default value 10


MaStatLab/LTN documentation built on Feb. 4, 2022, 10:35 p.m.